I haven't tried polychaining mine either, but then I only have a single OB-6 module.
6 notes playing and then 6 not means those second 6 notes are being sent to the slave and it's not receiving/playing them.
From RTMing, it seems that you only need to set polychain on the master, not the slave. Also, I would assume both synths need to be on the same MIDI channel. Lastly, on the master, is MIDI Out set to the correct port (MIDI or USB), as well as MIDI Sysex? How are the two synths connected? Assuming DIN MIDI from master to slave, you'd want to set both MIDI Out and MIDI SysEx to MIDI. Also, check Param Xmit and Param Rcv to make sure they match up on both synths.
I don't know if the master sends patch data to the slave when polychained, or if you have to do a patch dump to match them up. If the slave is in unison and the master in poly on the same patch, that could cause an issue as well.
I'm assuming you're using the OB-6 Keyboard as the master and the module as the slave? With Polychain turned off, do both synths play when you play the keyboard?